heatmapcommand.h

   1 #ifndef HEATMAPCOMMAND_H
   2 #define HEATMAPCOMMAND_H
   3
   4 /*
   5  *  heatmapcommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 3/25/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "inputdata.h"
  16 #include "sharedlistvector.h"
  17 #include "heatmap.h"
  18 #include "rabundvector.hpp"
  19
  20
  21 class HeatMapCommand : public Command {
  22
  23 public:
  24         HeatMapCommand(string);
  25         HeatMapCommand();
  26         ~HeatMapCommand(){}
  27
  28         vector<string> setParameters();
  29         string getCommandName()                 { return "heatmap.bin";                         }
  30         string getCommandCategory()             { return "OTU-Based Approaches";        }
  31         string getHelpString();
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36
  37 private:
  38         InputData* input;
  39         RAbundVector* rabund;
  40         vector<SharedRAbundVector*> lookup;
  41         vector<SharedRAbundFloatVector*> lookupFloat;
  42         HeatMap* heatmap;
  43
  44         bool abort, allLines;
  45         set<string> labels; //holds labels to be used
  46         string format, groups, sorted, scale, label, outputDir, sharedfile, relabundfile, listfile, rabundfile, sabundfile, inputfile;
  47         vector<string> Groups, outputNames;
  48         int numOTU, fontSize;
  49
  50
  51 };
  52
  53 #endif
  54